C1Net Workshop 3 on Metabolic Modelling
Under construction!
Though the overall structure is approximately right, titles of sessions and the linked resources are all likely to be revised.
Tutors
- David Fell (DF: Oxford Brookes University)
- Mark Poolman (MP: Oxford Brookes University)
- Noah Mesfin (NM: Oxford Brookes University)
- Rupert Norman (RN: University of Nottingham)
- Nicole Pearcy (NP: University of Nottingham)
Course Timetable and Resources Index
Day |
Time |
Place |
Activity |
Links |
Lecturer |
Monday |
12:00 |
|
Registration opens at St James Hotel |
|
|
23/1/17 |
12:30 |
|
Lunch |
|
|
|
13:30 |
|
Opening and introductions |
|
DF |
|
14:00 |
|
L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks. Outline of the week |
DF |
|
|
15:30 |
|
Tea/coffee |
|
|
|
16:00 |
|
L2. Computational representation of metabolic networks |
MP |
|
|
17:00 |
|
P1. Computers: checking internet connectivity, software installation. |
Installation of ScrumPy. |
DF, MP, NM,RN,NP |
|
18:00 |
|
Close and room registration (cont) |
|
|
|
|
|
|
|
|
|
19:00 |
|
Dinner |
|
|
|
|
|
|
|
|
Tuesday |
08:00 |
|
Breakfast |
|
|
16/12/14 |
09:00 |
|
L3. Sources of data for metabolic models |
DF |
|
|
10:00 |
|
L4. Null space and elementary modes |
DF |
|
|
10:30 |
|
Coffee/Tea |
|
|
|
11:00 |
|
P2. Python and ScrumPy |
DF, MP, NM,RN,NP |
|
|
12:30 |
|
Lunch |
|
|
|
13:30 |
|
L5. Biotechnological applications of metabolic network analysis |
DF |
|
|
14:30 |
|
P3. Null space analysis with ScrumPy |
As P2 plus these instructions |
DF, MP, NM,RN,NP |
|
15:30 |
|
Tea/Coffee |
|
|
|
16:00 |
|
L6. Linear Programming and Flux Balance Analysis |
MP |
|
|
17:00 |
|
P2 and P3 continued |
|
|
|
17:30 |
|
Close |
|
|
|
19:00 |
|
Dinner |
|
|
|
|
|
|
|
|
Wednesday |
08:00 |
|
Breakfast |
|
|
17/12/14 |
09:00 |
|
L7. Building genome-scale metabolic networks |
MP |
|
|
10:30 |
|
Coffee/Tea |
|
|
|
11:00 |
|
P4. Elementary modes of a simple model |
Instructions (To do: renumber practical header) |
DF, MP, NM,RN,NP |
|
12:30 |
|
Lunch + free time (Nottingham Castle and Caves?) |
|
|
|
15:30 |
|
Tea/Coffee |
|
|
|
15:45 |
|
L8. Examples of analyzing genome scale metabolic models |
MP or DF |
|
|
16:00 |
|
P5. Building models from MetaCyc with ScrumPy |
DF, MP, NM,RN,NP |
|
|
17:00 |
|
P5 continued |
|
|
|
18:00 |
|
Close |
|
|
|
19:00 |
|
Dinner |
|
|
|
|
|
|
|
|
Thursday |
08:00 |
|
Breakfast |
|
|
18/12/14 |
09:00 |
|
L9. Examples of genome scale modelling |
Slides |
NM, RN, NP |
|
10:30 |
|
Coffee/Tea |
|
|
|
11:00 |
|
P6. Flux Balance Analysis of fatty acid biosynthesis in E coli. |
DF, MP, NM,RN,NP |
|
|
12:30 |
|
Lunch |
|
|
|
13:30 |
|
L10. LP techniques for exploring genome scale models |
|
MP |
|
14:30 |
|
P6 continued |
|
DF, MP, NM,RN,NP |
|
15:30 |
|
Tea/Coffee |
|
|
|
16:00 |
|
P7. Analysing a genome scale model (E coli for fatty acid production?) |
Instructions TO DO: rework |
DF, MP, NM,RN,NP |
|
17:30 |
|
Close |
|
|
|
|
|
|
|
|
|
19:00 |
|
Workshop dinner |
|
|
|
|
|
|
|
|
Friday |
08:00 |
|
Breakfast |
|
|
19/12/14 |
09:00 |
|
P7 continued |
|
DF, MP, NM,RN,NP |
|
10:30 |
|
Coffee/Tea |
|
|
|
11:00 |
|
Discussion of results and prospective applications of modelling in attendees' projects |
|
DF, MP, NM,RN,NP |
|
12:00 |
|
Any questions? Closing remarks |
|
DF& MP |
|
12:30 |
|
(Sandwich?) lunch and departure |
|
|
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